Structural and thermodynamic analysis of thrombin:suramin interaction in solution and crystal phases

Suramin is a hexasulfonated naphthylurea which has been recently characterized as a non-competitive inhibitor of human alpha-thrombin activity over fibrinogen, although its binding site and mode of interaction with the enzyme remain elusive. Here, we determined two X-ray structure of the thrombin: suramin complex, refined at 2.4 angstrom resolution. While a single thrombin: suramin complex was found in the asymmetric unit cell of the crystal, some of the crystallographic contacts with symmetrically related molecules are mediated by both the enzyme and the ligand. Molecular dynamics simulations with the 1:1 complex demonstrate a large rearrangement of suramin in the complex, but with the protein scaffold and the more extensive protein-ligand regions keep unchanged. Small-angle X-ray scattering measurements at high micromolar concentration demonstrate a suramin-induced dimerization of the enzyme. These data indicating a dissimilar binding mode in the monomeric and oligomeric states, with a monomeric, 1:1 complex to be more likely to exist at the thrombin physiological, nanomolar concentration range. Collectively, close understanding on the structural basis for interaction is given which might establish a basis for design of suramin analogues targeting thrombin. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

sigma- and pi-defects at graphene nanoribbon edges: Building spin filters

The presence of certain kinds of defects at the edges of monohydrogenated zigzag graphene nanoribbons changes dramatically the charge transport properties inducing a spin-polarized conductance. Using an approach based on density functional theory and nonequilibrium Green`s function formalism to calculate the transmittance, we classify the defects in different classes depending on their distinct transport properties: (i) sigma-defects, which do not affect the transmittance close to the Fermi energy (E(F)); and (ii) pi-defects, which cause a spin polarization of the transmittance and that can be further divided into either electron or hole defects if the spin transport polarization results in larger transmittance for the up or down spin channel, respectively.